Renal Regulatory Elements and Methods of Use Thereof

ABSTRACT

Disclosed are cis-acting regulatory elements from a KIM-1 gene. The elements can be used to direct the expression of operably linked sequences in renal tissue.

STATEMENT OF GOVERNMENT INTEREST

This invention was made with federal government support under grant #DK 39773. The United States government has certain rights in the invention.

FIELD OF THE INVENTION

The invention relates generally to nucleic acids and more particularly to nucleic acids which can be used to direct expression in renal tissue of operably linked sequences.

BACKGROUND OF THE INVENTION

Significant interruption in kidney function in an individual can lead to incapacitation or even death. Disease or injury can impair kidney function. An example of an injury that can damage kidneys is ischemic injury. In this type of injury, kidney tissue is damaged because of oxygen deprivation occurring as a result of interruption of blood flow to the kidneys.

Certain agents involved in repair of diseased or damaged kidney tissue, and mechanisms in which the repair takes place, have been described. Mechanisms include induction of gene expression and recruitment of growth factors to the affected kidney tissue. Cell death and cellular proliferation are also associated with repair or kidney tissue.

Agents implicated in kidney tissue repair include polypeptides, e.g., growth factors such as insulin growth factor (IGF), epidermal growth factor (EGF), hepatocyte growth factor (HGF), and the endothelial cell adhesion molecule ICAM-1.

Recently, the polypeptide kidney-injury molecule (KIM-1) has been described. The expression of KIM-1 is increased in injured kidney tissue. The rat and human forms of this protein have been characterized. The KIM-1 cDNA sequence reveals that the KIM-1 protein is a type 1 membrane protein that contains a novel six-cysteine immunoglobulin-like domain and a mucin domain. The KIM-1 protein is a member of the immunoglobulin gene superfamily and most closely resembles mucosal addressin cell adhesion molecule 1 (MAdCAM-1).

SUMMARY OF THE INVENTION

It has been discovered that nucleic acid sequences in the vicinity of the human KIM-1 gene can be used to express linked sequences in renal tissue. Accordingly, the invention provides a cis-acting regulatory element useful for, inter alia, directing expression of an operatively linked sequence, e.g., a gene, in a mammal. The cis-acting KIM-1 regulatory sequence can also be used to identify trans-acting factors that mediate the response of the kidney to damaged or diseased tissue.

The invention provides an isolated nucleic acid that includes a cis-acting KIM-1 derived regulatory sequence. The nucleic acid can be, e.g., a nucleic acid sequence that includes the nucleic acid sequence of SEQ ID NOs:1, 2 or 3. The nucleic acid includes at least 5 contiguous nucleotides from a sequence that hybridizes to SEQ ID NOs: 1, 2, or 3, or sequences complementary to SEQ ID NOs: 1, 2, or 3. For example the regulatory sequence can include between 5 and 35 contiguous nucleotides from SEQ ID NO:3, or sequences complementary to such portions of SEQ ID NO:3.

In some embodiments, a cis-acting KIM-1 regulatory sequence according to the invention includes a portion of SEQ ID NOs:1, 2 or 3 sufficient to regulate kidney tissue-specific transcription of an operably linked sequence, e.g., an operably linked polypeptide-encoding sequence. A cis-acting KIM-1 regulatory sequence according to the invention can include a portion of SEQ ID NOs:1, 2 or 3 is sufficient to regulate kidney tissue-specific transcription following cellular injury e.g., anoxia or exposure to reactive oxygen species (“ROS”), or in a cell present in a confluent population of cells.

The invention also provides a cis-acting KIM-1 regulatory sequence operably linked to a sequence encoding a KIM-1 antisense nucleic acid. The cis-acting KIM-1 regulatory sequence can be operably linked to at least one polypeptide-encoding sequence and regulates renal tissue-specific transcription of the polypeptide-encoding sequence. For example, the polypeptide-encoding sequence may encode a KIM-1 polypeptide (e.g., a human KIM-1 polypeptide), or a non-KIM-1 polypeptide. This polypeptide can be, e.g., a cell survival-promoting factor, a cell growth-promoting factor, a wound-healing factor, an anti-fibrotic factor, an apoptosis-inhibiting factor, an anti-inflammatory factor, a terminal differentiation-promoting factor, a cell growth-inhibiting factor, an intravascular-volume restoration factor, a chelating agent, an alkylating agent, an angiotensin-converting enzyme-inhibiting factor, erythropoietin, a cytokine, a receptor, an anticoagulant, an enzyme, a hormone, an antibody, or a renal structural protein.

A cis-acting KIM-1 regulatory sequence according to the invention may be linked to, e.g., nucleic acid sequences encoding insulin growth factor (IGF), an epidermal growth factor (EGF), a fibroblast growth factor (FGF), a transforming growth factor beta (TGF β) Type II receptor, a hepatocyte growth factor (HGF), or an endothelial cell adhesion molecule ICAM-1.

The invention also provides a vector that includes a nucleic acid comprising a cis-acting KIM-1 regulatory sequence and cells containing these nucleic acids and vectors. The cell can be prokaryotic or eukaryotic. The cell can be, e.g. a metazoan organism or a unicellular organism, and can include, e.g., a fungal cell, yeast cell (such as Saccharomyces, Schizosaccharomyces, or Candida spp.), or a mammalian cell, e.g., a human, canine, bovine, porcine, feline, or rodent cell, or a non-human mammalian embryonic blastocyst cell.

The invention also provides a transgenic non-human mammal, e.g., a mouse, rat, goat, pig, cow, or sheep, containing an isolated cis-acting KIM1 regulatory sequence. The transgenic animal can be produced, e.g., by intrauterine implantation of a blastocyte cell containing a cis-acting KIM-1 regulatory sequence. The invention also includes one or more progeny of the transgenic non-human mammal DNA, wherein the progeny comprises the cis-acting DNA, or a fragment thereof.

The invention also provides a method of directing expression of a polypeptide. The method includes providing a cell, e.g., a renal cell, that includes an isolated cis-acting KIM-1 regulatory sequence operably linked to sequence encoding a polypeptide of interest, culturing the cell under conditions that allow for the expression of the polypeptide and expressing the polypeptide-encoding sequence.

The invention also includes a method of increasing transcription of a polypeptide-encoding sequence in tissue. The method includes providing a cell in the tissue that includes a cis-acting KIM-1 regulatory sequence linked to the polypeptide-encoding sequence and culturing the cell under conditions that allow for the transcription of the polypeptide-encoding sequence. The polypeptide-encoding sequence is then expressed, resulting in transcription of the polypeptide-encoding sequence in the tissue.

The invention also includes a method for identifying a test compound that modulates expression from a cis-acting KIM-1 derived regulatory sequence. The test compound can be contacted with a reporter construct that includes a reporter gene operably linked to an isolated cis-acting KIM-1 regulatory sequence. The level of expression of the reporter gene in the tissue is detected, e.g., measured. A change in the level of expression in the presence of the test compound relative to the level of expression in the absence of the test compound indicates that the test compound modulates the activity of the KIM promoter.

The invention also provides a method for delivering a therapeutic polypeptide to renal tissue of a subject. The method includes providing in the renal tissue a cell that includes a cis-acting KIM-1 regulatory sequence operably linked to a therapeutic polypeptide, and culturing the cell under conditions that allow for the expression of the polypeptide. The polypeptide-encoding sequence is expressed, thereby delivering the therapeutic polypeptide to the renal tissue of the subject.

The invention also includes a method for treating or preventing renal tissue injury. The method includes providing a cell that includes cis-acting KIM-1 regulatory sequence operably linked to a polypeptide coding sequence, and culturing the cell under conditions that allow for the expression of a therapeutic polypeptide-encoding sequence. The therapeutic polypeptide-encoding sequence is expressed, and the expressed polypeptide contacts the renal tissue, thereby treating or preventing renal tissue injury.

The invention also includes a method for increasing transcription of a nucleic acid in a subject by administering to the subject a cis-acting KIM-1 regulatory sequence operably linked to the nucleic acid and allowing for expression of the operably linked nucleic acid.

The invention also provides a method for treating or preventing renal tissue injury in a subject by administering to a subject in need thereof a cis-acting KIM-1 regulatory sequence operably linked to a sequence encoding a therapeutic polypeptide, in an amount sufficient to treat or prevent renal tissue injury in the subject.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

Other features and advantages of the invention will be apparent from the following detailed description, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-H are schematic representations of a nucleic acid sequence that includes a cis-acting KIM-1 regulatory sequence (SEQ ID NO:1).

FIGS. 2A-D are schematic representations of sequences from the 5′ region of the human KIM-1 gene.

FIG. 3 is a bar graph showing relative expression of luciferase in COS monkey kidney cells of various reporter constructs containing sequences from the 5′ region of the human KIM-1 gene

FIG. 4 is a bar graph showing relative expression of luciferase in LLCPK cells of various reporter constructs containing sequences from the 5′ region of the human KIM-1 gene.

FIG. 5 is a bar graph showing relative expression of luciferase in MDCK cells of various reporter constructs containing sequences from the 5′ region of the human KIM-1 gene.

FIG. 6 is a bar graph showing inducibility of sequences linked to a KIM-1 regulatory sequence in HK2 cells after exposure to reactive oxygen species (ROS) or anoxia.

FIG. 7 is a bar graph showing relative expression of luciferase in MDCK cells at various timepoints after transfection with reporter constructs containing sequences from the 5′ region of the human KIM-1 gene.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides a cis-acting regulatory element useful for, inter alia, directing expression of an operatively linked sequence, e.g., a gene, in a mammal. This cis-acting regulatory sequence from KIM-1 can also be used to identify trans-acting factors that mediate the response of the kidney to damaged or diseased tissue.

Sequence Identifier Numbers (SEQ ID NOs)

Sequence Identifier Numbers Used Herein Include the Following:

SEQ ID NO:1 corresponds to the nucleotide sequence of an 8933 bp human genomic DNA from the 5′ region of KIM-1 gene and is disclosed in FIGS. 1A-H. This fragment is present as a BamH1-BamH1 insert in the BamH1 site of the EMBL3 phage vector. The construct is named MZ007.

SEQ ID NO:2 corresponds to the nucleotide sequence of a 4.8 kb KpnI-KpnI fragment encompassing nucleotides 3796 to 8612 of the human KIM-1 insert in MZ007.

SEQ ID NO:3 corresponds to the nucleotide sequence of a 1.3 kb EcoR1-KpnI fragment encompassing nucleotides 7322-8612 of human KIM-1 insert in MZ007.

SEQ ID NO:4 corresponds to the nucleotide sequence of a 0.5 kb SacII-KpnI fragment encompassing nucleotides 8110-8612 of human KIM-1 insert in MZ007.

Cis-acting KIM-1 Derived Regulatory Sequences

Included in the invention is an isolated DNA that includes a cis-acting KIM-1 derived regulatory sequence. The term “isolated” refers to molecules separated from other DNA or RNA molecules, present in the natural source of the regulatory sequence. The term also refers to a nucleic acid or peptide that is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. An isolated nucleic acid includes nucleic acid fragments that are not naturally occurring as fragments and would not be found in the natural state. The term “isolated” is also used herein to refer to polypeptides that are isolated from other cellular proteins, and the term is meant to encompass both purified and recombinant polypeptides.

A cis-acting KIM-1 derived regulatory sequence, also termed herein “cis-acting regulatory element”, “regulatory element”, or “regulatory sequence”, includes nucleic acid sequence elements derived from sequences in the vicinity of a mammalian KIM-1 gene that are capable of modulating transcription from a basic promoter, as well as enhancers or silencers. The terms “promoter” and “regulatory element” further encompass “tissue specific” promoters and regulatory elements, i.e., promoters and regulatory elements which bring about expression of an operably linked DNA sequence preferentially in specific cells (e.g., cells of a renal tissue). Gene expression occurs preferentially in a specific cell if expression in this cell type is significantly higher than expression in other cell types. The terms “promoter” and “regulatory element” also encompass so-called “leaky” promoters and “regulatory elements”, which regulate expression of a selected DNA primarily in one tissue, but cause expression in other tissues as well. The terms “promoter” and “regulatory element” also encompass non-tissue specific promoters and regulatory elements, i.e., promoters and regulatory elements which are active in most cell types.

A promoter or regulatory element can be a constitutive promoter or regulatory element, i.e., a promoter or regulatory element which constitutively regulates transcription, or it can be a promoter or regulatory element which is inducible, i.e., a promoter or regulatory element which is active primarily in response to a stimulus. A stimulus can be, e.g., a physical stimulus, such as injury (e.g., ischemia), and/or a molecule, such as a hormone, a cytokine, a heavy metal, phorbol esters, cyclic AMP (cAMP), or retinoic acid.

The term “enhancer”, also referred to herein as “enhancer element”, includes regulatory elements capable of increasing, stimulating, or enhancing transcription from a basic promoter. The term “silencer”, also referred to herein as “silencer element” is intended to include regulatory elements capable of decreasing, inhibiting, or repressing transcription from a basic promoter. The terms “promoter” and “regulatory element” further encompass “tissue specific” promoters and regulatory elements, i.e., promoters and regulatory elements which effect expression of the selected DNA sequence preferentially in specific cells (e.g., cells of a specific tissue). Gene expression occurs preferentially in a specific cell if expression in this cell type is significantly higher than expression in other cell types.

In some embodiments, one or more copies of a cis-acting regulatory element is present within a transcribed region of a KIM-1 gene. In other embodiments, the cis-acting regulatory element is located 5′ to the transcriptional start site of a KIM-1 gene.

In some embodiments, a cis-acting regulatory sequence is operably linked sequence to a promoter that is not derived from the native KIM-1 gene, and to a heterologous sequence, such as a polypeptide-encoding sequence. In other embodiments, the cis-acting regulatory sequence is operably linked to a KIM-1 promoter sequence and a heterologous sequence, such as a polypeptide-encoding sequence.

In some embodiments, the cis-acting regulatory sequence includes the 1.3 kb sequence of SEQ ID NO:3, e.g., the regulatory sequence can include the nucleotides of SEQ ID NO:1 and SEQ ID NO:2, as well as SEQ ID NO:3. In other embodiments, the cis-acting regulatory sequence includes a portion of SEQ ID NO:3 that is sufficient to confer renal tissue expression of an operably linked sequence which otherwise would not be expressed in renal tissue. For example, the cis-acting regulatory sequence may include at least 5, 10, 15, 20, 25, 30, 35, 50, 100, 125, or 150 contiguous nucleotides from SEQ ID NO:3, or sequences complementary to SEQ ID NO:3. Thus, if desired, sequences responsible for conferring renal cell-specific expression in the sequence of SEQ ID NO:3 can be localized more precisely. Localization can be performed using methods well-known in the art, e.g., by constructing plasmids containing successively smaller portions of the 1.3 kb fragment of SEQ ID NO:3 placed upstream of a luciferase reporter gene in a construct such as pGL3 Basic (Promega Corporation, Madison, Wis.), or in any of the many reporter genes known in the art. The construct is then transfected into kidney cells. Suitable kidney cells include, e.g., COS, LLC/PK1, and MDCK cells. Increased expression of the reporter gene in kidney cells compared to the expression of the starting construct alone indicates that the smaller test fragment of the 1.3 kb DNA allows for renal tissue expression. Higher expression of the test fragment in renal tissue as compared to other cell types (i.e., fibroblast cells or non-smooth muscle cells) indicates that the DNA directs polypeptide expression in a renal tissue-specific manner.

Similarly, in other embodiments, the cis-acting regulatory sequence is sufficient to confer both inducible (e.g., upon exposure to a stimulus) and tissue-specific expression in injured renal tissue. For example, the sequence can include at least the portion or portions of SEQ ID NO: 2 that are necessary and sufficient for such expression. Such portion(s) can be localized routinely as described above.

KIM-1 cis-sequences according to the invention can be used to direct expression of linked sequences following injury or under various conditions. For example, a nucleotide sequence that includes SEQ ID NO:2 (the 4.8 kb KpnI-KpnI fragment) can be used to direct expression of a linked polypeptide in cells that have been subjected to injury using a reactive oxygen species (“ROS”), or subjected to injury because of anoxia. A nucleotide sequence that includes at least the relevant portion or portions of SEQ ID NO:2 can also be used to direct expression of a sequence of interest in confluent cells.

In another embodiment, the isolated nucleic acid includes a cis-acting KIM-1 derived regulatory sequence that has been modified, e.g., by adding, deleting, or substituting one or more nucleic acid residues. Such modifications can modulate the regulatory or transcriptional activity of the regulatory element. For example, a modification can increase or decrease the activity of a promoter or regulatory element. A modification can also affect the tissue specificity or inducibility of a promoter or regulatory element.

Desired modifications of a regulatory element according to the present invention can be performed according to methods well known in the art, such as by mutagenesis. The activity of the modified promoter or regulatory element can then be tested, using the herein described methods for assaying the cis-acting activity of a KIM-1 regulatory sequence.

In some embodiments, the regulatory sequence is inducible. As used herein, “inducible” means that the regulatory sequence affects expression of a linked sequence in response to a stimulus. The stimulus can be physical, e.g., stress, such as heat shock, anoxia, or pressure, or chemical. Examples of chemical stimuli include, e.g., a hormone, a cytokine, a heavy metal, phorbol esters, cyclic AMP (cAMP), or retinoic acid. In preferred embodiments, the regulatory sequence is inducible by injury, e.g., ischemic injury, or ischemia. As used herein, “ischemia” means having a blood flow at least 10% below that which is normal for an individual of similar size and age, as measured under resting conditions or exercise conditions. In an adult human, normal resting blood flow is approximately 1 ml/min/gram of myocardial mass. During exercise, blood flow typically rises to approximately 3-6 ml/min/gram of myocardial mass. Ischemia may be associated with a physical would or blow, sudden loss of blood volume, toxicity, or a physical obstruction such as a tumor.

Other types of injury include, e.g., injury due to hypertension, chemotherapy (e.g., injury due to cisplatin damage), chronic renal failure, injury due to auto-immune disorders (e.g., lupus), or polycystic kidney (PCK) disease.

In some embodiments, the regulatory sequence preferentially directs expression of an operably linked sequence in renal tissue. The term “operably linked” means that the regulatory sequence is associated with the nucleic acid in such a manner as to facilitate transcription of the nucleic acid. In some embodiments, the operably linked nucleic acid encodes an antisense nucleic acid. The antisense nucleic acid can be a portion of the anti-sense strand of a gene whose expression is intended to be decreased in a renal tissue. For example, for conditions characterized by undesired proliferation of kidney tissue, the DNA may be a KIM-1 antisense nucleic acid.

In other embodiments, the DNA is operably linked to at least one polypeptide-encoding sequence. The polypeptide sequence can be, e.g., one encoded by a KIM-1 cDNA. Examples of nucleic acids encoding rat and human KIM-1 cDNAs, and their corresponding encoded amino acid sequences are provided in PCT publication WO97/44460.

Alternatively, the DNA is operably linked to nucleic acid that encodes a polypeptide other than KIM1. For example, the polypeptide can be a therapeutic factor such as insulin growth factor (IGF), epidermal growth factor (EGF), fibroblast growth factor (FGF), transforming growth factor beta (TGF β) Type II receptor, particularly the soluble fragment of TGF β receptor, hepatocyte growth factor (HOF), and the endothelial cell adhesion molecule ICAM-1. Other therapeutic polypeptides include factors such as a cell survival-promoting factor, a cell growth-promoting factor, a wound-healing factor, an anti-fibrotic factor, an apoptosis-inhibiting factor, an anti-inflammatory factor, a terminal differentiation-promoting factor, a cell growth-inhibiting factor, an intravascular-volume restoration factor, a chelating agent, an alkylating agent, an angiotensin-converting enzyme-inhibiting factor, erythropoietin, a cytokine, a receptor, an anticoagulant, an enzyme, a hormone, an antibody, and a renal structural protein.

A nucleic acid to be transcribed from a KIM-1 derived regulatory element can also be linked to a reporter gene. A reporter gene is any gene encoding a protein, the amount of which can be determined. Exemplary reporter genes include the luciferase gene, e.g., the bacterial luciferase gene, e.g., the luciferase gene present in pGL3-basic (Promega Corp., Madison, Wis.). Other suitable reporter genes include the beta-galactosidase gene (LacZ), the chloramphenicol acetyl transferase (CAT) gene, or any gene encoding a protein providing resistance to a specific drug.

The regulatory elements disclosed herein can also be used to prepare probes and primers based on KIM-1 derived regulatory sequences. These probes and primers can be used, e.g., to identify KIM-1 genomic regions in a subject, such as a human. The probes can be provided in the form of a probe or primer that includes a region of nucleotide sequence that hybridizes under stringent conditions to at least approximately 6, 8, 10 or 12, preferably about 25, 30, 40, 50 or 75 consecutive nucleotides of any of SEQ ID NOS: 1, 2, 3, or 4.

The probe optionally includes an attached label, which is capable of being detected. The label can be, e.g., radioisotopes, fluorescent moieties, enzymes, and enzyme co-factors.

The cis-acting regulatory sequences, including the probe or primer molecules, can also be used as a part of a diagnostic test kit, for example, to detect mutations in the promoter, which result in faulty expression of a renal gene or a gene associated with renal tissue.

Nucleic acids, including nucleic acid fragments, containing or derived from cis-acting KIM-1 regulatory sequences can be prepared according to methods well known in the art and described, e.g., in Sambrook, J. Fritsch, E. F., and Maniatis, T. (1989) MOLECULAR CLONING: A LABORATORY MANUAL, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. For example, discrete fragments of the regulatory element can be prepared and cloned using restriction enzymes. Alternatively, discrete fragments can be prepared using the Polymerase Chain Reaction (PCR) using primers having an appropriate sequence, such as a sequence in SEQ ID NO: 1. The activity of promoter fragments can be tested in vitro in transfection assays or in vivo in transgenic animals described herein. Also within the scope of the invention are nucleic acids that are homologues or equivalents of the above-described nucleic acids.

Cis-acting KIM-1 derived regulatory sequences can be isolated from other organisms by using a KIM-1 cDNA to screen genomic DNA sequences in the organism of interest, and then testing the genomic sequences in promoter-reporter assays as described herein. Preferably, the KIM-1 cDNA used for the screening is from the same, or closely related organism. Thus, to isolate a murine KIM-1 derived cis-regulatory sequence, the murine KIM-1 cDNA is used. Preferably, the probe is derived from a 5′ region of the KIM-1 cDNA.

Vectors and Cells Containing cis-acting KIM-1 Derived Regulatory Sequences

This invention also provides vectors, e.g., expression vectors that include cis-acting KIM-1 derived regulatory sequences.

In some embodiments, the expression vector includes a recombinant gene encoding a KIM-1 or a therapeutic polypeptide. Such expression vectors can be used to transfect cells and thereby produce protein. Constructs containing cis-acting KIM-1 derived regulatory sequences can also be used as a part of a gene therapy protocol to deliver nucleic acids in vitro or in vivo to particular cell types (e.g., kidney).

The vector can include any vector known in the art for propagating a desired nucleic acid in a cell of interest. Thus, the vector can be chosen to propagate a nucleic acid that includes a cis-acting KIM-1 derived regulatory sequences in a prokaryotic or eukaryotic host, or both. In some embodiments, the vector is a viral vector, e.g., a retroviral vector. For a review, see Miller, A. D. (1990) Blood 76:271. Protocols for producing recombinant retroviruses and for infecting cells in vitro or in vivo with such viruses can be found, e.g., in CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Ausubel, F. M. et al. (eds.) Greene Publishing Associates, (1989), Sections 9.10-9.14 and other standard laboratory manuals. Examples of suitable retroviruses include pLJ, pZIP, pWE and pEM.

Vectors can alternatively be adenovirus-derived vectors, e.g., those described in Berkner et al. (1988) BioTechniques 6:616; Rosenfeld et al. (1991) Science 252:431-434; and Rosenfeld et al. (1992) Cell 68:143-155. Suitable adenoviral vectors derived from the adenovirus strain Ad type 5 d1324 or other strains of adenovirus (e.g., Ad2, Ad3, Ad7 etc.) are well known to those skilled in the art.

The vector can be derived from an adeno-associated virus (AAV). Adeno-associated virus is a naturally occurring defective virus that requires another virus, such as an adenovirus or a herpes virus, as a helper virus for efficient replication and a productive life cycle. For a review see Muzyczka et al. Curr. Topics in Micro and Immunol. (1992) 158:97-129. It is also one of the few viruses that can integrate its DNA into non-dividing cells, and exhibits a high frequency of stable integration (see for example Flotte et al. (1992) Am. J. Respir. Cell. Mol. Biol. 7:349-356; Samulski et al. (1989) J. Virol. 63:3822-3828; and McLaughlin et al. (1989) J. Virol. 62:1963-1973). See also U.S. Pat. No. 5,872,154. Other suitable vectors include those based in the human immunodeficiency virus (HIV). These vectors are described in, e.g., U.S. Pat. No. 5,665,577 and U.S. Pat. No. 5,981,276.

Vectors can be introduced into cells using methods known in the art. In addition to viral transfer methods, such as those illustrated above, non-viral methods can also be used to introduce a gene. These methods include, e.g., calcium phosphate precipitation, microparticle-mediated delivery, and biolistic transformation. In some embodiments, delivery can rely on endocytic pathways for the uptake of genes by the targeted cell. Exemplary targeting means of this type include liposomal derived systems, poly-lysine conjugates, and artificial viral envelopes.

Delivery can be performed using nucleic acids entrapped in liposomes bearing positive charges on their surface (e.g., lipofectins) and (optionally) which are tagged with antibodies against cell surface antigens of the target tissue. See, e.g., Mizuno et al. (1992) No Shinkei Geka 20:547-551; PCT publication WO91/06309; Japanese patent application 1047381; and European patent publication EP-A-43075. For example, lipofection of cells can be carried out using liposomes tagged with monoclonal antibodies against any cell surface antigen present on a hepatic cell, such as an asialoglycoprotein receptor.

Cells containing cis-acting KIM-1 regulatory sequences, or vectors that include cis-acting KIM-1 regulatory sequences as described herein, can be any cell known in the art. Thus, they can include prokaryotic cells (e.g., E. coli cells) or eukaryotic calls. Eukaryotic cells can include single-celled organisms such, e.g. yeast (e.g., Saccharomyces cerevisiae or Schizosaccharomyces pombe). Alternatively, the cells can be mammalian cells, e.g., human or simian cells. In some embodiments, the cells are kidney cells, or cell lines derived from kidney cells.

Transgenic Animals Containing cis-Acting KIM-1 Regulatory Sequences

The invention also includes transgenic non-human vertebrates, e.g., mammals and birds, that contain cis-acting KIM-1 regulatory sequences.

For example, some embodiments, a host cell of the invention is a fertilized oocyte or an embryonic stem cell into which exogenous cis-acting KIM-1 regulatory sequences have been introduced. Such host cells can be used to create non-human transgenic vertebrate animals in which exogenous cis-acting KIM-1 regulatory sequences have been introduced into their genome or homologous recombinant animals in which endogenous cis-acting KIM-1 regulatory sequences have been altered. Such animals are useful for studying the function and/or activity of cis-acting KIM-1 regulatory sequences and for identifying and/or evaluating modulators of cis-acting KIM-1 regulatory sequences. As used herein, a “transgenic animal” means a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more of the cells of the animal includes a transgene. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, zebrafish, amphibians, etc. A transgene is exogenous DNA that is integrated into the genome of a cell from which a transgenic animal develops and that remains in the genome of the mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal. As used herein, a “homologous recombinant animal” is a non-human animal, preferably a mammal, more preferably a mouse or a rat, in which an endogenous cis-acting KIM-1 regulatory sequences has been altered by homologous recombination between the endogenous gene and an exogenous DNA molecule introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal.

A transgenic animal of the invention can be created by introducing cis-acting KIM-1 regulatory sequences into the male pronuclei of a fertilized oocyte, e.g., by microinjection, retroviral infection, or the like, and allowing the oocyte to develop in a pseudopregnant female foster animal. For example, a cis-acting KIM-1 regulatory sequence having the nucleic acid sequence of SEQ ID NO:3, or a functional fragment thereof, can be introduced as a transgene into the genome of a non-human animal. Alternatively, a nonhuman homologue of the human cis-acting KIM-1 regulatory sequences, such as a cis-acting KIM-1 regulatory sequence, can be isolated based on hybridization to the human cis-acting KIM-1 regulatory sequences (described further above) and used as a transgene. Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene. Methods for generating transgenic animals via embryo manipulation and microinjection, particularly animals such as mice, have become conventional in the art and are described, for example, in U.S. Pat. Nos. 4,736,866; 4,870,009; and 4,873,191; and Hogan, MANIPULATING THE MOUSE EMBRYO, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1996). Similar methods are used for production of other transgenic animals. A transgenic founder animal can be identified based upon the presence of the transgenic cis-acting KIM-1 derived regulatory sequences in its genome and/or expression of sequences operably linked to the transgenic cis-acting KIM-1 derived regulatory sequences. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene carrying a transgenic cis-acting KIM-1 derived regulatory sequence can further be bred to other transgenic animals carrying other transgenes.

To create a homologous recombinant animal, a vector is prepared which contains at least a portion of a cis-acting KIM-1 regulatory sequences gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the cis-acting KIM-1 regulatory sequences. The cis-acting KIM-1 regulatory sequence can be a human sequence (e.g., SEQ ID NO:3), but more preferably, is a non-human homologue of a human cis-acting KIM-1 regulatory sequence. For example, a mouse homologue of human cis-acting KIM-1 regulatory sequence of SEQ ID NO:3 can be used to construct a homologous recombination vector suitable for altering a cis-acting KIM-1 regulatory sequence in the mouse genome.

In one embodiment, the vector is designed such that, upon homologous recombination, the endogenous a cis-acting KIM-1 regulatory sequence is functionally disrupted (i.e., no longer encodes a functional protein; also referred to as a “knock out” vector).

Alternatively, the vector can be designed such that, upon homologous recombination, the endogenous cis-acting KIM-1 regulatory sequence is mutated or otherwise altered but is still functional (e.g., the upstream regulatory region can be altered to thereby alter the expression of the endogenous cis-acting KIM-1 regulatory sequence). In the homologous recombination vector, the altered portion of the cis-acting KIM-1 regulatory sequence is flanked at its 5′ and 3′ ends by additional nucleic acid of the cis-acting KIM-1 regulatory sequence to allow for homologous recombination to occur between the exogenous cis-acting KIM-1 regulatory sequence carried by the vector and an endogenous cis-acting KIM-1 regulatory sequence in an embryonic stem cell. The additional flanking cis-acting KIM-1 regulatory sequence is of sufficient length for successful homologous recombination with the endogenous gene. Typically, several kilobases of flanking DNA (both at the 5′ and 3′ ends) are included in the vector. See e.g., Thomas et al. (1987) Cell 51:503 for a description of homologous recombination vectors. The vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced cis-acting KIM-1 regulatory sequence has homologously recombined with the endogenous cis-acting KIM-1 regulatory sequence are selected (see e.g., Li et al. (1992) Cell 69:915).

The selected cells are then injected into a blastocyst of an animal (e.g., a mouse) to form aggregation chimeras. See e.g., Bradley 1987, In: TERATOCARCINOMAS AND EMBRYONIC STEM CELLS: A PRACTICAL APPROACH, Robertson, ed. IRL, Oxford, pp. 113-152. A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term. Progeny harboring the homologously recombined DNA in their germ cells can be used to breed animals in which all cells of the animal contain the homologously recombined DNA by germline transmission of the transgene. Methods for constructing homologous recombination vectors and homologous recombinant animals are described further in Bradley (1991) Curr Opin Biotecinol 2:823-829; PCT International Publication Nos.: WO 90/11354; WO 91/01140; WO 92/0968; and WO 93/04169.

In another embodiment, transgenic non-human animals can be produced that contain selected systems that allow for regulated expression of the transgene. One example of such a system is the cre/loxP recombinase system of bacteriophage P1. For a description of the cre/loxP recombinase system, see, e.g., Lakso et al. (1992) PNAS 89:6232-6236. Another example of a recombinase system is the FLP recombinase system of Saccharonyces cerevisiae (O'Gorman et al. (1991) Science 251:1351-1355. If a cre/loxP recombinase system is used to regulate expression of the transgene, animals containing transgenes encoding both the Cre recombinase and a selected protein are required. Such animals can be provided through the construction of “double” transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.

Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut et al. (1997) Nature 385:810-813. In brief, a cell, e.g., a somatic cell, from the transgenic animal can be isolated and induced to exit the growth cycle and enter G₀ phase. The quiescent cell can then be fused, e.g., through the use of electrical pulses, to an enucleated oocyte from an animal of the same species from which the quiescent cell is isolated. The reconstructed oocyte is then cultured such that it develops to morula or blastocyst and then transferred to pseudopregnant female foster animal. The offspring borne of this female foster animal will be a clone of the animal from which the cell, e.g., the somatic cell, is isolated.

Identifying Trans-Acting Factors that Bind to cis-Acting KIM1-Derived Regulatory Sequences

Also provided are methods of identifying compounds that bind to cis-acting KIM-1-derived regulatory sequences. These compounds include trans-acting factors can include, e.g., polypeptides such as transcription factors, which interact preferentially with cis-acting KIM-1 regulatory sequences, or small molecules.

In one embodiment, a compound is identified by performing assays in which a cis-acting KIM-1 nucleic acid sequence is incubated with a test compound. Binding of the compound to the nucleic acid is detected using methods known in the art for assessing nucleic acid binding. For example, binding can be measured using electrophoretic mobility shift assays (EMSA). One way in which an EMSA can be prepared is to incubate together a DNA, which is preferably labeled, containing a KIM-1-derived cis-acting regulatory sequence and the test compound. The mixture is then subjected to electrophoresis, and the migration of the labeled nucleic acid in the presence of the test compound is compared to the migration of the labeled nucleic acid in the absence of the test compound. A difference in mobility indicates that the test compound binds to regulatory sequence.

Any suitable compound can be used as the test compound. In some embodiments, the test compound is obtained from a cellular extract known to contain, or to be suspected of containing, a trans-acting factor. Suitable cells include kidney cells, e.g., Cos cells.

Cell-based methods can also be used to identify compounds that modulate activity. For example, a cell containing a cis-acting KIM-1-derived regulatory sequence operably linked to a nucleic acid encoding a reporter molecule is contacted with a test compound and the reporter molecule mRNA or translated product is measured. mRNA levels and protein levels can be determined using any method known in the art, e.g. using Northern blot hybridization analysis, immunoprecipitations, or immunohistochemistry.

The trans-acting factors can also be identified using in vivo assays. For example, a reporter construct can be constructed in which a reporter gene is under the control of any of the cis-acting KIM-1-derived regulatory sequences disclosed herein.

The reporter gene can be any gene encoding a suitably detectable protein. The reporter gene can be, e.g., a gene encoding luciferase. Cells are transfected with the reporter construct that includes a cis-acting KIM-1 regulatory element. Transfection can be transient or stable. The cells can be transfected with more than one reporter construct. The transfected cells can then be incubated in the presence or absence of a test compound for an appropriate amount of time and the level of expression of the reporter gene is determined.

Similar assays can also be performed using a cell or nuclear extract instead of cells. Thus, in one embodiment, the invention provides a method for identifying a compound which modulates KIM activity. The method includes incubating a reporter construct that includes any of the regulatory elements according to the invention with a nuclear or cellular extract, or isolated nuclei, in the presence or absence of test compound. Expression of the test compound is then measured, e.g., by including a labeled nucleotide in the reaction and measuring the amount of label incorporated in the product transcribed from the reporter construct. Other methods can also be used to determine the amount of reporter gene expression in this system, such as the measure of the amount of protein expressed by the reporter gene.

In yet another embodiment, compounds that modulate the regulatory elements of the present invention in vivo can be identified in non-human animals. In one embodiment of the invention, a non-human animal, e.g., a mouse, is treated with a compound, such as a compound identified in one of the assays described above. After an appropriate amount of time, the level of activity is determined and compared to its activity in a mouse that has not received the test compound.

Pharmaceutical Compositions Containing cis-Acting KIM-1 Regulatory Sequences

Pharmaceutical compositions containing cis-acting KIM-1 regulatory sequences can be formulated in a conventional manner using one or more physiologically acceptable carriers or excipients.

Administration can be parenteral, intravenous, subcutaneous, intramuscular, retroperitoneal, intracranial, intraorbital, ophthalmic, intraventricular, intracapsular, intraspinal, intracistemal, intraperitoneal, transmucosal, or oral. The Nucleic acids can be provided in compositions formulated in various ways, according to the corresponding route of administration. For example, liquid solutions can be made for ingestion or injection. Gels or powders can be made for ingestion, inhalation, or topical application. Methods for making such formulations are well known and can be found in standard references in the field, for example, REMINGTON'S PHARMACEUTICAL SCIENCES, Mack Publishing Company, Easter, Pa., 15th Edition (1975).

The compositions can also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.

The compositions can be presented in a pack or dispenser device that may contain one or more unit dosage forms containing the active ingredient. The pack may for example comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration.

The therapeutic compositions can also contain a carrier or excipient. Useful excipients include buffers (for example, citrate buffer, phosphate buffer, acetate buffer, and bicarbonate buffer), amino acids, urea, alcohols, ascorbic acid, phospholipids, proteins (for example, serum albumin), EDTA, sodium chloride, liposomes, mannitol, sorbitol, and glycerol.

Methods for Using cis-Acting KIM-1 Regulatory Sequences

Cells containing cis-acting KIM-1 regulatory sequences operably linked to a polypeptide-encoding sequence can be used to direct expression of the polypeptide. For example, the polypeptide can be expressed by providing a cell containing a KIM-1 regulatory sequence and culturing the cell, if necessary, to allow for expression of the polypeptide. Any cell type can be used as long as it allows for expression of the polypeptide-encoding sequence operably linked to the cis-acting regulatory sequence. In preferred embodiments, the cell is a renal cell.

In some embodiments, the expressed polypeptide is isolated. If desired, the polypeptide-encoding sequence can include a sequence encoding a signal sequence to allow for secretion of the polypeptide. The polypeptide can then be isolated from the extracellular medium.

The cis-acting KIM-1 regulatory sequences can also be used to increase transcription of an operably linked sequence in vitro or in vivo, e.g., in a cell, tissue or subject (such as a human). The operably linked sequence can be, e.g., a polypeptide-encoding sequence or an antisense nucleic acid construct. To increase transcription, a cell containing a cis-acting KIM-1 regulatory sequence operably linked to the sequence of interest, or a tissue containing two or more of such cells, is cultured under conditions that allow for the expression of the operably linked sequence to allow for increased levels of transcripts corresponding to the operably linked sequence in the cell or tissue. “Culture” as used herein can include in vitro culture under conditions necessary for maintaining the viability of mammalian cells, or in situ culture of cells in the body of an animal.

In another embodiment, the cis-acting KIM-1 regulatory sequences are used to direct expression of a nucleic acid sequence that is not normally under the control of such regulatory sequences. A nucleic acid molecule containing a cis-acting KIM-1 regulatory sequence is integrated into the genome of a target cell in the vicinity of a gene of interest. The gene of interest is preferably one that is normally not expressed in renal tissue, or is expressed at low amounts in renal tissue. Integration of the introduced cis-acting KIM-1 regulatory sequence near the gene of interest allows for the expression of the gene of interest under the control of the KIM-1 regulatory sequence. Preferably, the cis-acting KIM-1 regulatory sequences are introduced near the 5′ region of the gene of interest.

Another use of the cis-acting KIM-1 regulatory sequences is to deliver a therapeutic polypeptide to renal tissue of a subject. To deliver the polypeptide, a cell including a cis-acting KIM-1 regulatory sequence operably linked to a therapeutic polypeptide-nucleic acid sequence is introduced into renal tissue. The sequences are expressed, e.g., by culturing the cell under conditions that allow for the expression of the linked polypeptide, to result in the delivery of the therapeutic polypeptide to the subject's renal tissue. In some embodiments, the therapeutic polypeptide linked to the cis-acting KIM-1 regulatory sequence is expressed following a stimulus. The stimulus can be, e.g., an injury such as ischemic injury or is ischemic reperfusion injury, or some other nephrotoxic injury.

The cis-acting KIM-1 regulatory sequences can also be used in a method for treating or preventing renal tissue injury in a subject. The method can include providing a cell in the subject that includes an introduced cis-acting KIM-1 regulatory sequence operably linked to a nucleic acid encoding a therapeutic nucleic acid, e.g., a therapeutic polypeptide-encoding sequence. The nucleic acid is allowed to express, and the gene product thereby introduced to the renal tissue to prevent or treat renal tissue injury in the subject. The cis-acting KIM-1 regulatory sequence can be introduced into the subject using methods described in the art for introducing nucleic acid sequences into cells. The nucleic acids can be introduced ex vivo or in vivo.

For gene therapy or antisense therapy, the claimed DNA may be introduced into target cells of an animal, e.g., a patient, using standard vectors and/or gene delivery systems. Suitable gene delivery systems may include liposomes, receptor-mediated delivery systems, naked DNA, and viral vectors such as herpes viruses, retroviruses, adenoviruses, and adeno-associated viruses, among others. Delivery of nucleic acids to a specific site in the body for gene therapy or antisense therapy may also be accomplished using a biolistic delivery system, such as that described by Williams et al., 1991, Proc. Natl. Acad. Sci. U.S.A. 88:2726-2729. Standard methods for transfecting cells with isolated DNA are well known to those skilled in the art of molecular biology. Gene therapy and antisense therapy to prevent or decrease the development kidney disease or injury may be carried out by directly administering the claimed DNA to a patient or by transfecting renal cells with the claimed DNA ex vivo and infusing the transfected cells into the patient.

A therapeutically effective amount is an amount of the DNA of the invention that is capable of producing a medically desirable result in a treated animal. As is well known in the medical arts, dosages for any one patient depends upon many factors, including the patient's size, body surface area, age, the particular compound to be administered, sex, time and route of administration, general health, and other drugs being administered concurrently. Dosages will vary, but a preferred dosage for intravenous administration of DNA is from approximately 10⁶ to 10²² copies of the DNA molecule.

Nucleic acids can be delivered to a subject by any of a number of routes, e.g., as described in U.S. Pat. Nos. 5,399,346 and 5,580,859. Delivery can thus also include, e.g., intravenous injection, local administration, and systemic administration (see U.S. Pat. No. 5,328,470) or stereotactic injection (see e.g., Chen et al. (1994) PNAS 91:3054-3057).

The pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can include a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells that produce the gene delivery system.

EXAMPLES

The following examples illustrate particular non-limiting embodiments of the invention.

Example 1 Cloning and Characterization of KIM-1 Derived Sequences

Cis-acting KIM-1 derived regulatory sequences were identified by screening a human genomic library with a 220 bp Not1-Kpn1 DNA fragment containing sequences in the 5′ region of the human KIM-1 cDNA. The human KIM-1 cDNA is described generally in PCT publication WO97/44460 and Ichimura et al., J. Biol. Chem. 273:4135-42, 1998.

The screening identified a genomic fragment of 8933 bp (SEQ ID NO:1). The sequence of the 8933 bp region is shown in FIGS. 1A-1H. A translational start codon is present beginning at nucleotide 8655.

A 4817 bp KpnI-KpnI fragment (SEQ ID NO:2), which corresponds to nucleotides 3796-8612 of FIGS. 1A-1H, was subcloned into a luciferase-encoding pGL3b expression vector (Promega Corp.) and named p4.8KIM/pGL3b. The p4.8KIM/pGL3K construct is shown schematically in FIG. 2B. The presence of the 4817 bp KpnI-KpnI fragment in the pLUC3 was found to increase levels of encoded luciferase in renal cells, as is explained in more detail in the Examples, below.

A smaller sequence able to increase expression of luciferase in kidney cells was identified by subcloning a 1289 bp EcoR1-KpnI fragment (SEQ ID NO:3) corresponding to nucleotides 7322-8612 in FIG. 1 into a pLUC3 vector. The resulting construct was named 1.3pKIM-1, and is shown schematically in FIG. 2C.

A construct named 0.5pKIM, a pLUC3-based construct including only nucleotides 8110 to 8612 (SEQ ID NO:4) of FIG. 1, did not increase levels of luciferase as compared to expression. However, even though the region 8110 to 8612 is inactive alone, sequences present within the region may nevertheless be required, along with other sequences, to confer renal cell expression of linked sequences.

Example 2 Expression in Kidney Cells of Reporter Sequences Operably Linked to KIM-1 Derived Sequences

Human genomic sequences from the 5′ region of the human KIM-1 gene were tested for their ability to direct expression of a reporter polypeptide in three kidney-derived cell lines COS cells, a cell line derived from African green monkey kidney fibroblasts; LC/PK cells, a cell line derived porcine kidney epithelial cell lines; and MDCK cells, a cell line derived from canine kidney epithelial cells.

The cell lines were transiently transfected with constructs containing various regions of DNA from the human KIM-1 gene linked to a reporter luciferase gene. These constructs were concomitantly transfected with pCMV driven β-galactosidase vectors to standardize transfection efficiency, and activity of luciferase and β-galactosidase was measured. Activities were calculated as luciferase/β-gal ratios. Relative activities were calculated as the ratio of construct activity to negative control, i.e., promoterless luciferase vector (pGL3b).

DEAE-mediated transfection was used to introduce constructs (described in more detail below) into cell lines. Transfection was performed at 80% confluence, about 24 hours after seeding cells.

DNA was introduced into the cells by aspirating medium from the cells and mixing 10 ml of the appropriate culture medium (including 10% Nu serum, Collaborative Biomedical Products, #51004), 400 μl of DEAE (1×PBS+10 mg/ml DEAE Dextran+2.5 mM Chloroquine), and 20 μg of DNA (10 μg luciferase construct, 2 μg/β-gal vector, 8 μg BlueScript Vector).

Cells were exposed to DNA for 2-4 hours, after which the DNA solution was removed by aspiration and replaced with 5 ml 10% DMSO in 1×PBS. After 2 minutes, this solution was removed and the cells were washed twice with 1×PBS. Fresh medium was added, and cells were harvested after 48 hours.

Cells were washed once with 1×PBS, then incubated with 500 μl of 1×PBS. Cells were collected and centrifuged for 2 minutes, after which the supernatant was removed. Cells were resuspended in 200 μl of 0.25M TRIS, pH 7.8, and subjected to 3 shock freeze-thaw cycles, then centrifuged for 5 minutes at 14,000 g. The supernatant was used for luciferase and β Galactosidase assays.

To measure β-galactosidase activity, 25 μl of supernatant, 30 μl of 10×Mg buffer (90 mM MgCl₂. 1.02M beta-mercaptoethanol), 60 μl of 40 mM CPRG, and 48 μl of 0.5 sodium phosphate pH 7.5 were mixed and incubated until a red color developed. 500 μl of 1M Na₂CO₃ was added, and the OD at 570 nm was measured.

To measure luciferase activity 25 μl (p10) of the supernatant were mixed with 50 μl of 2× assay buffer, as per the manufacturer's instructions (Catalog # E 1502, Promega Corporation, Madison, Wis.). Measurements were made using a photoluminometer.

The KIM-1 human genomic region used to generate the constructs is shown in FIG. 2A. Constructs used in the transfection assays are shown in FIGS. 2B-2D. An 8933 bp fragment (SEQ ID NO:1) is shown schematically in FIG. 2A in a 5′ to 3′ orientation. KpnI sites are located at positions 3796 and 8612 as shown in the figure. For reference, the ATG initiation codon of the human KIM-1 occurs at position 8655.

The tested sequences are shown schematically in FIGS. 2B-2D. One tested sequence included a 4816 bp KpnI-KpnI fragment from the 5′ flanking region of the human KIM-1 gene. This fragment corresponds to the sequences bordered by KpnI sites at positions 3796 and 8612 of MZ007. FIG. 2B illustrates a construct made by inserting the 4816 bp KpnI-KpnI fragment into a pLUC3 Basic expression vector (Promega Corporation). The resulting construct was named 4.8 pKIM/PGL3b.

A shorter fragment from the 4816 bp KpnI-KpnI region was also tested. This fragment was defmed by an EcoRI-KpnI fragment encompassing nucleotides 7322-8611 of MZ007. This KpnI fragment was inserted into the pLUC3 Basic expression vector and named 1.3pKIM/pGL3b. This construct is shown schematically in FIG. 2C.

A still shorter fragment defined by a SacII-KpnI fragment encompassing nucleotides 8110-8612 of MZ007 was also examined. This construct was named 0.5pKIM/pGL3b and is shown schematically in FIG. 2D.

For each cell line tested, relative luciferase activities were calculated by measuring luciferase following transfection with no plasmid (i.e., zero, “0”), the pGL3 Basic vector alone (“pGL3”), or the constructs 4.8pKIM/pGL3b, 1.3pKIM/pGL3b, and 0.5pKIM/pGL3b.

For transformations into COS cells, DMEM was used as the culture medium. For the 4.8pKIM construct, four trials were performed, each using 2 plates. The RA was 3.8, with SD of 2.82. For the 1.3 pKIM construct, four trials were performed, each using 2 plates. The RA was 6.3, with an SD of 4.19. For the 0.5 pKIM construct, 2 trials were performed, each using 2 plates. The RA as 3.3, with an SD of 1.54. The results of the transfection assays using the COS cells are shown in FIG. 3.

For transformations into LLC-PK cells, DMEM was used as the culture medium. For the 4.8pKIM/PGL3b construct, three trials were performed, each using 2 plates. The RA was 5.5, with a SD of 1.43. For the 1.3pKIM/PGL3b construct, three trials were performed, each using 2 plates. The RA was 3.4, with an SD of 0.89. For the 0.5pKIM/PGL3b construct, two trials were performed, using 2 plates each. The RA was 1.5, with an SD of 0.34. The results of the transfection assays using LLC-PK cells are summarized in FIG. 4.

For transformations into MDCK cells, MEM was used as the culture medium. For the 4.8pKIM construct, 3 trials were performed, using 2 plates each. The relative activity (RA) was 7.0, and the SD was 3.46. For the 1.3 pKIM/PGL3b construct, 3 trials were performed, each using 2 plates. The relative activity was 3.4, with a SD of 0.89. The results for the transfection assays using MDCK cells are shown in FIG. 5.

In assays using COS cells (FIG. 3), LLC/PK1 cells (FIG. 4), and MDCK cells (FIG. 5), luciferase activity was significantly higher in cells transfected with the constructs 4.8pKIM/pGL3b and 1.3pKIM/pGL3b as compared to cells transfected with pGL3 alone, and cells not transfected with any construct.

These results indicate that sequences nucleotides 7322-8612 as shown in FIGS. 1A-H contain cis-acting regulatory elements that are able to increase expression of operably liked sequences in kidney tissues. Additional elements that increase this activity may be in 3796-7322 region, as is shown in FIG. 6, as is discussed in Example 3, below.

The 0.5pKIM/pGL3b construct did not increase expression of luciferase relative to cells transfected with pGL3 alone in the cell types tested. While these results suggest that these KIM-1 derived sequences did not confer expression of linked sequences, at least in the cell lines and conditions used, these results do not exclude the possibility that this region of the KIM-1 flanking region contains elements that are necessary or important for increasing expression of linked sequences in kidney tissues.

Example 3 Expression in Kidney Cells of Reporter Sequences Operably Linked to KIM-1 Derived Sequences Following Injury

Expression of luciferase encoded by 4.8pKIM, 1.3 pKIM, and 0.5 pKIM was measured in transfected HK2 cells that had been subjected to chemical anoxia using cyanide and deoxyglucose. HK2 cells are derived from epithelial proximal tubule cells from human kidney.

A 12-well plate system (MULTIWELL™ 12-well, Becton-Dickson) was used in these studies. The culture medium used was EGM (Clontech). Prior to transformation, 2 ml medium per well was added to the cells, then removed by aspiration. HK2 cells were seeded at a density of 30,000/well. Cells reached 80% confluence after 16-24 hours.

DNA was prepared by mixing 50 μl of serum free medium, 5 μg of DNA (2.5 μg luciferase construct, 0.5 μg β-galactosidase vector, 2 μg BlueScript vector), and 5 μg of SUPERFECT reagent (Qiagen Corp.), and incubating for 7 minutes. 300 μl of medium+10% FCS was added, and the mix was then added to the cells. The cells were then allowed to incubate for 2 hours. The DNA solution was next removed by aspiration, after which the cells were washed twice in 1×PBS, after which the cells were incubated in culture medium with 10% FCS.

To induce chemical anoxia, medium was removed by aspiration, and cells were washed once with 1×PBS. Cells were then incubated for 90 minutes in 1 ml Krebs-Henseleit buffer (“KHB”) (6.72 mM NaCl, 3.6 mM KCl, 1.3 mM KH2PO4, 25 mM NaHCO₃, 1 mM CaCl₂, a mM MgCl₂, ph7.4 in incubator), along with 5 mM sodium cyanide and 5 mM deoxyglucose. Cells were then washed once with 1×PBS and incubated in KHB+10 mM dextrose for 15-20 minutes, then harvested as explained below.

For harvesting, cells were washed once in 1×PBS, then incubated for 5 minutes with 200 μl 25 mM GlyGly, 15 mM MgSO4, 4 mM EGTA, pH 8.0, 1% Triton X 100, 1 mM DTT. Lysate was then removed from the wells and used for luciferase and β galactosidase assays.

To assay for β galactosidase activity, 50 μl of cell extract was mixed with 50 μl of assay buffer (Catalog # E2000, Promega Corporation, Madison, Wis.), followed by incubation at 37° C. until a faint yellow color developed. Signals were then measured in an ELISA reader at 405 nm.

Luciferase activity was measured by mixing 50 μl of 2× assay buffer as indicated by the manufacturer (Catalog #E1502, Promega, Madison, Wis.). Measurements were made using a photoluminometer.

Luciferase expression was measured in three different populations of transfected HK2 cells. The first group included cells not subjected to chemical anoxia. These cells were assayed 72 hours following transfection. The second group included cells assayed 72 hours following transfection and 90 minutes after inducement of chemical anoxia. For each group of cells, separate populations of cells were transfected with 4.8pKIM/pGL3b, 1.3pKIM/GL3b, and 0.5pKIM/pGL3b.

The results are illustrated in FIG. 6. For baseline cells, the 4.8pKIM/pGL3b construct yielded a RA of 9.1, with a SEM of 1.1. The 1.3pKIM/pGL3b construct yielded a RA of 5.0, with a SEM of 0.8. The 0.5 pKIM constructed yielded a RA of 1.6, with a SEM of 0.2.

In cells subjected to chemical anoxia, the 4.8pKIM/pGL3b generated a RA of 13.5, with a SEM of 1.5. The 1.3pKIM/pGL3b construct yielded a RA of 5.6, with a SEM of 0.4. The 0.5pKIM/pGL3b construct generated a RA of 2.0, with a SEM of 0.3.

These data demonstrate that KIM-1 sequences present in the 4.8pKIM/pGL3b construct caused higher levels of expression of the linked luciferase gene in cells subjected to anoxia, as compared to control cells. This effect was not seen with the 1.3pKIM/pGL3b and 0.5pKIM/pGl3b constructs in this experiment.

Example 4 Expression in Confluent Kidney Cells of Reporter Sequences Operably Linked to KIM-1 Derived Sequences

Expression of a luciferase gene linked to 4.8pKIM/PGL3b, 1.3pKIM/PGL3b, or 0.5pKIM/PGL3b in confluent cells was investigated.

MDCK cells were transfected with the indicated construct 16-24 hours after seeding. Transfected cells were harvested after 24, 48, and 72 hours, and luciferase and β-galactosidase activity was then measured. The results are summarized below: TABLE 1 RA SD 24 hours, 80% confluence 4.8pKIM/PGL3b 5.65 0.97 1.3pKIM/PGL3b 4.93 2.07 0.5pKIM/PGL3b 2.03 .98 48 hours, 90% confluence 4.8pKIM/PGL3b 13.55 3.5 1.3pKIM/PGL3b 7.95 1.91 0.5pKIM/PGL3b 2.4 .61 72 hours, 100% confluence 4.8pKIM/PGL3b 31.8 6.5 1.3pKIM/PGL3b 9.83 4.82 0.5pKIM/PGL3b 1.93 1.09

These results demonstrated that KIM-1 sequences present in 4.8pKIM/pGL3B lead to significantly higher levels of luciferase as cells reach confluency. KIM-1 sequences present only in the 1.3pKIM/pGL3B and 0.5pKIM/pGL3B constructs did not increase expression of luciferase in these studies.

Example 5 Use of KIM-1-Derived cis-Acting Regulatory Sequences in Gene Therapy

KIM-1 derived cis-acting regulatory sequences according to the invention can be used for gene therapy treatment of renal diseases. KIM-1 cis-acting regulatory sequences can be used alone or as part of a vector to express heterologous genes, e.g., a KIM-1 cDNA, or a protein other than a KIM-1 polypeptide, in renal cells.

The DNA or vector containing a KIM-1 cis-acting regulatory sequence linked to a nucleic acid encoding a polypeptide of interest is introduced into renal cells, which in turn produce the polypeptide of interest. For example, sequences encoding the desired polypeptide may be operably linked to the renal cell-specific promoter sequences of the invention and expressed in renal cells.

Example 6 Use of KIM-1-Derived cis-Acting Regulatory Sequences in Antisense Therapy

The KIM-1 cis-acting regulatory sequence is used in methods of antisense therapy. Antisense therapy is carried out by administering to an animal, e.g., a human patient, DNA containing the renal cell-specific promoter sequences of the invention operably linked to a DNA sequence, i.e., an antisense template, which is transcribed into an antisense RNA. The antisense RNA is a short nucleotide sequence (generally at least 10 nucleotides, preferably at least 14 nucleotides, and up to 100 or more nucleotides) formulated to be complementary to a portion of a specific mRNA sequence. The antisense template is preferably located downstream from the promoter sequences of the invention. A poly A tail element is typically located at the end of the antisense sequence to signal the end of the sequence. Standard methods relating to antisense technology have been described. See, e.g., Melani et al., Cancer Res. 51:2897-2901, 1991. Following transcription of the DNA sequence into antisense RNA, the antisense RNA binds to its target mRNA molecules within a cell, thereby inhibiting translation of the mRNA and down-regulating expression of the protein encoded by the mRNA.

The expression of other renal cell proteins may also be inhibited in a similar manner. For example, the DNA of the invention can be operably linked to antisense templates that are transcribed into antisense RNA capable of inhibiting the expression of the following proteins: TGF-β, dysfunctional collagen mutant genes, WT-1 (Wilms Tumor gene), and genes associated with polycystic kidney disease (PCK).

OTHER EMBODIMENTS

While the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

1. An isolated DNA comprising a cis-acting KIM-1 derived regulatory sequence.
 2. The DNA of claim 1, wherein said DNA comprises SEQ ID NO:3.
 3. The DNA of claim 1, wherein said DNA comprises SEQ ID NO:2.
 4. The DNA of claim 1, wherein said regulatory sequence preferentially directs expression of an operably linked sequence in renal tissue.
 5. The DNA of claim 1, wherein said regulatory sequence is inducible.
 6. The DNA of claim 5, wherein said regulatory sequence is inducible by injury.
 7. The DNA of claim 6, wherein said injury is ischemic.
 8. The DNA of claim 1, wherein said DNA comprises at least 5 contiguous nucleotides from SEQ ID NO:3, or sequences complementary to SEQ ID NO:3.
 9. The DNA of claim 1, wherein said DNA comprises at least 5 contiguous nucleotides from a sequence that hybridizes with SEQ ID NO:3, or sequences complementary to SEQ ID NO:3.
 10. The DNA of claim 8, wherein said DNA comprises between 5 and 35 contiguous nucleotides from SEQ ID NO:3, or sequences complementary to SEQ ID NO:3.
 11. The DNA of claim 9, wherein said DNA comprises between 5 and 35 contiguous nucleotides from a sequence that hybridizes with SEQ ID NO:3, or sequences complementary to SEQ ID NO:3.
 12. The DNA of claim 1, wherein said DNA is operably linked to a sequence encoding a KIM-1 antisense nucleic acid.
 13. The DNA of claim 1, wherein the DNA is operably linked to at least one polypeptide-encoding sequence and regulates renal tissue-specific transcription of said polypeptide-encoding sequence
 14. The DNA of claim 13, wherein said DNA comprises a portion of SEQ ID NO:3 that is sufficient to regulate kidney tissue-specific transcription of said polypeptide-encoding sequence.
 15. The DNA of claim 13, wherein said regulatory sequence is inducible.
 16. The DNA of claim 13, wherein said polypeptide-encoding sequence encodes a KIM-1 polypeptide.
 17. The DNA of claim 16, wherein said KIM-1 polypeptide comprises the amino acid sequence of a human KIM-1 polypeptide.
 18. The DNA of claim 13, wherein said polypeptide-encoding sequence does not encode a KIM-1 polypeptide.
 19. The DNA of claim 13, wherein said polypeptide-encoding sequence encodes a therapeutic polypeptide.
 20. The DNA of claim 13, wherein said polypeptide is selected from the group consisting of a cell survival-promoting factor, a cell growth-promoting factor, a wound-healing factor, an anti-fibrotic factor, an apoptosis-inhibiting factor, an anti-inflammatory factor, a terminal differentiation-promoting factor, a cell growth-inhibiting factor, an intravascular-volume restoration factor, a chelating agent, an alkylating agent, an angiotensin-converting enzyme-inhibiting factor, erythropoietin, a cytokine, a receptor, an anticoagulant, an enzyme, a hormone, an antibody, and a renal structural protein.
 21. The DNA of claim 13, wherein said polypeptide is selected from the group consisting of an insulin growth factor (IGF), an epidermal growth factor (EGF), a fibroblast growth factor (FGF), a transforming growth factor beta (TGF β) Type II receptor, a hepatocyte growth factor (HGF), and an endothelial cell adhesion molecule ICAM-1.
 22. A vector comprising the DNA of claim
 1. 23. A cell comprising the vector of claim
 22. 24. The cell of claim 23, wherein said cell is a unicellular organism.
 25. The cell of claim 23, wherein said cell is a yeast cell.
 26. The cell of claim 23, wherein said cell is a mammalian cell.
 27. The cell of claim 23, wherein said cell is a human cell.
 28. The cell of claim 23, wherein said cell is a non-human mammalian embryonic blastocyst cell.
 29. A transgenic non-human mammal produced by intrauterine implantation of said blastocyte comprising said cell of claim
 28. 30. One or more progeny of said transgenic mammal of claim 29, wherein the DNA of said progeny comprises said DNA of claim 1, or a fragment thereof.
 31. A method of directing expression of a polypeptide, said method comprising: a) providing a cell comprising the DNA of claim 13; b) culturing said cell under conditions that allow for the expression of said polypeptide; and c) expressing said polypeptide-encoding sequence; thereby directing expression of said polypeptide.
 32. The method of claim 31, wherein said cell is a renal cell.
 33. A method of increasing transcription of a polypeptide-encoding sequence in tissue, said method comprising: a) providing in said tissue a cell comprising the DNA of claim 13; b) culturing said cell under conditions that allow for the transcription of said polypeptide-encoding sequence; and c) expressing said polypeptide-encoding sequence; thereby providing increased transcription of said polypeptide in said tissue.
 34. A method for identifying a test compound that modulates expression from a cis-acting KIM-1 derived regulatory sequence, said method comprising: a) contacting said test compound and a reporter construct comprised of a reporter gene, operably linked to said DNA of claim 1; and b) detecting the level of expression of said reporter gene; wherein a change in the level of expression relative to the level of expression in the absence of said test compound indicates that said test compound modulates the activity of said KIM promoter.
 35. A method for delivering a therapeutic polypeptide to renal tissue of a subject, said method comprising: a) providing in said renal tissue a cell comprising the DNA of claim 13; b) culturing said cell under conditions that allow for the expression of said polypeptide; and c) expressing said polypeptide-encoding sequence; thereby delivering said therapeutic polypeptide to said renal tissue of said subject.
 36. The method of claim 35, wherein said stimulus is injury.
 37. The method of claim 36, wherein said injury is an ischemia-reperfusion injury.
 38. The method of claim 36, wherein said injury is a nephrotoxic injury.
 39. A method for treating or preventing renal tissue injury, the method comprising: a) providing a cell comprising the DNA of claim 13; b) culturing said cell under conditions that allow for the expression of a therapeutic polypeptide-encoding sequence; c) expressing said therapeutic polypeptide-encoding sequence; and d) contacting said tissue with said cell expressing said therapeutic polypeptide-encoding sequence; thereby treating or preventing renal tissue injury.
 40. A method for increasing transcription of a nucleic acid in a subject, the method comprising administering to said subject the DNA of claim 4, wherein said operably linked DNA is expressed in an amount sufficient to result in increased transcription of said operably linked nucleic acid.
 41. A method for treating or preventing renal tissue injury in a subject, the method comprising administering to said subject in need thereof the DNA of claim 13, wherein said operably linked DNA is expressed in an amount sufficient to treat or prevent renal tissue injury in said subject. 